Bio::SeqEvolution::DNAPoint implements the simplest evolution model:nucleotides change by point mutations, only. Transition/transversionrate of the change, rate(), can be set.The new sequences are named with the id of the reference sequenceadded with a running number. Placing a new sequence into a factory tobe evolved resets that counter. It can also be called directly withreset_sequence_counter.The default sequence type returned is Bio::PrimarySeq. This can bechanged to any Bio::PrimarySeqI compliant sequence class.Internally the probability of the change of one nucleotide is mappedto scale from 0 to 100. The probability of the transition occupiesrange from 0 to some value. The remaining range is divided equallyamong the two transversion nucleotides. A random number is thengenerated to pick up one change.Not that the default transition/transversion rate, 1:1, leads toobserved transition/transversion ratio of 1:2 simply because there isonly one transition nucleotide versus two transversion nucleotides.

Transition/transversion ratio is an observed attribute of an sequencecomparison. We are dealing here with the transition/transversion ratethat we set for our model of sequence evolution.Note that we are using standard nucleotide alphabet and that there canthere is only one transition versus two possible transversions. Rate 2is needed to have an observed transition/transversion ratio of 1.

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